This application requests support for the acquisition of a hybrid Quadrupole, Ion Mobility separation, orthogonal acceleration Time-of-Flight Tandem Mass Spectrometer (Synapt HDMS), interfaced with a fully integrated ultra-high performance liquid chromatography (nanoAcquityUPLC) platform from Waters Corporation. This state-of-the-art instrument will be utilized as a shared research resource in the Cornell Proteomics and Mass Spectrometry (MS) Facility and will be essential to 28 active NIH supported grants. There is a growing interest in proteomics and MS at Cornell, as is evidenced by the exponential growth in the number of samples processed by the facility over the past 3 years (Figure 2). The proposed instrument will complement the existing instrumentation in Cornell, particularly with respect to its applications for analysis of intact protein complexes, protein-protein/ligand interactions and probing protein conformation. This highly sensitive and accurate mass instrument will provide capabilities in protein domain mapping and peptide mapping resulting in confident identification of protein modifications and better de-novo sequencing of proteins for which there is no available genome sequence. This high resolution instrument will be critical to the success of quantitative proteomics studies using stable isotope labeling (SILAC and iTRAQ). The power of UPLC separation combining with MSE scan feature improves the dynamic range of the instrument enhancing the identification of low abundance proteins and enables label-free comparative proteomics. Furthermore, the instrument includes both ion mobility and Time Aligned Parallel (TAP) fragmentation features which will provide increased specificity and more confident structural characterization of proteins and other bio-molecules. The particular strengths of the proposed instrument are: i) Ion Mobility separation which provides a means to estimate molecular size, shape and charge in addition to mass;ii) TAP fragmentation for structural characterization;iii) High mass accuracy (<2 ppm RMS via the LockSpray), high resolution (17,500) and wide dynamic range (4 orders of linearity) critical for improved data quality;iv) High duty cycle and fast TDC (4GHz) for fast data acquisition rates;v) Wide m/z range (100,000 m/z) for TOF analyzer capable of analysis >1,000 kDa protein complexes;vi) UPLC-MS/MS with MSE mode for a parallel data acquisition enabling sensitive analysis of complex samples with a wide dynamic concentration of analytes. The proposed instrument will enhance the electrospray MS technologies available in the core facility. The acquisition of this instrument will have an enormous impact on more than two dozens of NIH-funded research projects, and will improve the research infrastructure of Cornell University and the education/training programs of students and researchers. It will accelerate and facilitate a wide range of research projects of Cornell faculty across six colleges relevant to life sciences research, and help to maintain Cornell's competitive position. PUBLIC HEALTH RELEVANCE: The relevance of this application to public health is established through the 28 odd NIH supported research programs that would benefit from the acquisition of this instrumentation. The instrumentation requested herein possesses technical abilities that far exceed those that are currently available to these researchers and thus would allow them to accomplish the goals of these funded projects through the gathering of more and better data. The improved quality and quantity of data gathered in connection with these projects is critical to the achievement of the public health goals for which each was granted priority funding.